Phenotype and GWAS Information:

Agronomic Traits

Note: All the agronomic trait is from the article Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collection.

Metabolic Traits

Note: All the metabolic trait is from the article Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism. Some metabolics have two replications, the second replication is end with '_2', like 'mr1002_2'.

Search Results:

The detailed information about mr1221 can be find at here.

GWAS Results:

Note: If the P-value of Linear Regression (LR) or Linear Mixed Model (LMM) ≤ 1e-5 or the rank ≤ 20000, the results are saved. Only the LMM results are plotted below.

Significant Candidate Loci (Lead SNP):

Variation IDVariation ID V6ChromosomePositionLR P-value LMM P-value
vg0610410261 sf0610409262 6 10410261 9.18E-75 4.08E-20
vg0610461143 sf0610460144 6 10461143 5.08E-71 2.04E-23
vg0612914787 sf0612913788 6 12914787 5.72E-57 4.81E-09
vg0610644321 sf0610643322 6 10644321 1.37E-56 4.75E-19
vg0612996928 sf0612995929 6 12996928 2.19E-54 6.61E-08
vg0617359224 sf0617358227 6 17359224 5.03E-51 1.09E-06
vg0718993703 sf0718992710 7 18993703 2.70E-47 NA
vg0629122299 sf0629121301 6 29122299 4.36E-44 3.08E-09
vg0719491051 sf0719490058 7 19491051 1.74E-38 4.76E-07
vg0610590324 sf0610589325 6 10590324 9.78E-38 2.14E-10
vg0610278393 sf0610277394 6 10278393 NA 7.08E-12
vg0611735326 sf0611734327 6 11735326 NA 2.74E-10
vg0610788671 sf0610787672 6 10788671 NA 7.53E-09
vg0611957068 sf0611956069 6 11957068 NA 1.04E-08
vg0611744358 sf0611743359 6 11744358 NA 1.14E-07
vg0610028912 sf0610027913 6 10028912 NA 1.96E-07
vg0610681498 sf0610680499 6 10681498 NA 2.09E-07
vg0234591868 sf0234585999 2 34591868 NA 2.52E-07
vg0611575099 sf0611574100 6 11575099 NA 3.77E-07
vg0610787522 sf0610786523 6 10787522 NA 8.57E-07
vg0610792532 sf0610791533 6 10792532 NA 9.32E-07
vg0610102626 sf0610101627 6 10102626 NA 1.04E-06
vg0903984961 sf0903983961 9 3984961 NA 2.17E-06
vg1216521167 sf1216518460 12 16521167 NA 2.79E-06